#!/usr/bin/env python
# coding: utf-8

# This notebook is not currently set up to work standalone. See [@gregcaporaso](http://github.com/gregcaporaso)'s [slides from SciPy 2016](http://bit.ly/qiime2-scipy2016) for more information. See http://2.qiime.org if you'd like to try QIIME 2. 
# 
# Installation steps prior to demo:
# ```bash
# conda create -n q2-scipy2016 python=3.5 q2-diversity q2cli -c qiime2 -c biocore -c bioconda
# source activate q2-scipy2016
# ```
# 
# Download example Artifacts (QIIME 1 data files can be imported as QIIME 2 Artifacts, see [Importing data](https://github.com/qiime2/qiime2/wiki/Importing-data)): 

# In[1]:


get_ipython().system('rm -rf *.qza *.qzv feature-table-frequency q2-demo-sample-md.tsv')
get_ipython().system('curl -sO https://raw.githubusercontent.com/qiime2/q2-types/master/q2_types/tests/data/feature-table-frequency.qza')
get_ipython().system('curl -sO https://raw.githubusercontent.com/qiime2/q2-types/master/q2_types/tests/data/phylogeny.qza')
get_ipython().system('curl -sO https://dl.dropboxusercontent.com/u/2868868/q2-demo-sample-md.tsv')


# # Artifacts

# In[2]:


from qiime import Artifact


# In[3]:


table = Artifact.load('./feature-table-frequency.qza')
table


# In[4]:


tree = Artifact.load('./phylogeny.qza')


# In[5]:


import biom
biom_table = table.view(biom.Table)
biom_table


# In[6]:


import pandas as pd
table.view(pd.DataFrame)[:5]


# In[7]:


get_ipython().system('unzip feature-table-frequency.qza')


# # Executing actions defined by plugins

# In[8]:


import qiime.plugins
import pprint
pprint.pprint(qiime.plugins.available_plugins())


# In[9]:


import qiime.plugins.feature_table
import qiime.plugins.diversity


# In[10]:


table100 = qiime.plugins.feature_table.actions.rarefy(table, counts_per_sample=100)
dm = qiime.plugins.diversity.actions.beta_phylogenetic(table100, tree, metric='unweighted_unifrac')


# (Note: alternatives to rarefaction, such as those discussed in [McMurdie *et al.* (2014)](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531), are planned for addition as a plugin.)

# In[11]:


dm


# Provenance is very basic at this stage, but it is being improved in alpha ([qiime2/qiime2#88](https://github.com/qiime2/qiime2/issues/88)).

# In[12]:


dm.provenance


# In[13]:


table100.save('table100.qza')
dm.save('dm.qza')


# # Types help users use QIIME correctly

# Passing an incorrect type results in a ``TypeError``:

# In[14]:


qiime.plugins.diversity.actions.beta_phylogenetic(table, tree, 'unweighted_unifrac')


# # Command line interface (``q2cli``) demo commands
# 
# ```bash
# qiime 
# qiime info
# qiime diversity --help
# qiime diversity beta_phylogenetic --help
# qiime diversity pcoa --help
# qiime diversity pcoa --distance-matrix dm.qza --pcoa pc
# conda install q2-emperor -c qiime2 -c biocore -c bioconda
# qiime info
# ```
# 
# See [Installing and using QIIME 2](http://2.qiime.org/Installing-and-using-QIIME-2) documentation.

# # QIIME Studio demo
# 
# ```
# cd qiime-studio-0.0.1
# npm start
# ```
# 
# Then, through the UI, change to the directory where the previous demos were run. (During alpha, we will transition so this can be started as a normal desktop application, e.g., with a QIIME icon.)
# 
# See [QIIME Studio](http://2.qiime.org/QIIME-studio) documentation.

# In[ ]: